comparison emboss_fuzzpro.xml @ 11:0e2484b6829b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author iuc
date Mon, 30 Jan 2017 13:27:40 -0500
parents 9b98d3d903c6
children 27c43fb015f0
comparison
equal deleted inserted replaced
10:9b98d3d903c6 11:0e2484b6829b
1 <tool id="EMBOSS: fuzzpro38" name="fuzzpro" version="5.0.0"> 1 <tool id="EMBOSS: fuzzpro38" name="fuzzpro" version="5.0.0.1">
2 <description>Protein pattern search</description> 2 <description>Protein pattern search</description>
3 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> 3 <macros>
4 <command>fuzzpro -sequence $input1 -outfile $out_file1 -pattern "$pattern" -pmismatch $mismatch -rformat2 $out_format1 -auto</command> 4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <code file="emboss_format_corrector.py" />
8 <command>fuzzpro -sequence '$input1' -outfile '$out_file1' -pattern '$pattern' -pmismatch $mismatch -rformat2 $out_format1 -auto</command>
5 <inputs> 9 <inputs>
6 <param format="data" name="input1" type="data"> 10 <param name="input1" type="data" format="data" label="Sequences" />
7 <label>Sequences</label> 11 <param name="pattern" type="text" value="" label="Search pattern">
8 </param>
9 <param name="pattern" type="text" value="">
10 <sanitizer> 12 <sanitizer>
11 <valid initial="string.printable"> 13 <valid initial="string.printable">
12 <remove value="&apos;"/> 14 <remove value="&apos;"/>
13 </valid> 15 </valid>
14 <mapping initial="none"> 16 <mapping initial="none">
15 <add source="&apos;" target=""/> 17 <add source="&apos;" target=""/>
16 </mapping> 18 </mapping>
17 </sanitizer> 19 </sanitizer>
18 <label>Search pattern</label>
19 </param> 20 </param>
20 <param name="mismatch" type="text" value="0"> 21 <param name="mismatch" type="integer" value="0" label="Number of mismatches" />
21 <label>Number of mismatches</label> 22 <param name="out_format1" type="select" label="Output report file format">
22 </param>
23 <param name="out_format1" type="select">
24 <label>Output Report File Format</label>
25 <option value="seqtable">SeqTable</option> 23 <option value="seqtable">SeqTable</option>
26 <option value="embl">EMBL</option> 24 <option value="embl">EMBL</option>
27 <option value="genbank">GENBANK</option> 25 <option value="genbank">GENBANK</option>
28 <option value="gff">GFF</option> 26 <option value="gff">GFF</option>
29 <option value="pir">PIR</option> 27 <option value="pir">PIR</option>
39 <option value="table">Table</option> 37 <option value="table">Table</option>
40 <option value="tagseq">TagSeq</option> 38 <option value="tagseq">TagSeq</option>
41 </param> 39 </param>
42 </inputs> 40 </inputs>
43 <outputs> 41 <outputs>
44 <data format="fuzzpro" name="out_file1" /> 42 <data name="out_file1" format="fuzzpro" />
45 </outputs> 43 </outputs>
46 <code file="emboss_format_corrector.py" />
47 <help> 44 <help>
48 You can view the original documentation here_. 45 You can view the original documentation here_.
49
50 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/fuzzpro.html
51 46
52 ------ 47 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/fuzzpro.html
53
54 **Citation**
55
56 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. &lt;http://www.ncbi.nlm.nih.gov/pubmed/10827456&gt;`_
57
58 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. &lt;http://www.ncbi.nlm.nih.gov/pubmed/17568012&gt;`_
59 </help> 48 </help>
49 <expand macro="citations" />
60 </tool> 50 </tool>